X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;h=3f67c4c50eff86bdc190c73c4d70537abb7bef0f;hb=47fd498a6fe7d2e3350a9e87c526bf1e59d00be5;hp=6f9a864382d0b2a7422ff614f63ddcd14ecd7fc5;hpb=7596cd64543481df859a9bd2e73a3b3bb6b2e42c;p=jalview.git

diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 6f9a864..3f67c4c 100644
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -21,6 +21,7 @@
 package jalview.ws.sifts;
 
 import jalview.api.DBRefEntryI;
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Sequence;
@@ -67,7 +68,7 @@ public class SiftsClientTest
 
   @BeforeTest(alwaysRun = true)
   public void populateExpectedMapping() throws SiftsException
-   {
+  {
     expectedMapping.put(51, new int[] { 1, 2 });
     expectedMapping.put(52, new int[] { 2, 7 });
     expectedMapping.put(53, new int[] { 3, 12 });
@@ -165,11 +166,13 @@ public class SiftsClientTest
     expectedMapping.put(145, new int[] { 95, 714 });
     expectedMapping.put(146, new int[] { 96, 722 });
     expectedMapping.put(147, new int[] { 97, 729 });
-   }
-   
+  }
+
   @BeforeTest(alwaysRun = true)
   public void setUpSiftsClient() throws SiftsException
   {
+    // read test props before manipulating config
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
     // test reproducibility
     new SiftsSettings();
@@ -233,7 +236,6 @@ public class SiftsClientTest
     }
   }
 
-
   @Test(groups = { "Functional" })
   public void getAllMappingAccessionTest()
   {
@@ -257,8 +259,7 @@ public class SiftsClientTest
     try
     {
       HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
-              "A", testSeq,
-              null);
+              "A", testSeq, null);
       Assert.assertEquals(testSeq.getStart(), 1);
       Assert.assertEquals(testSeq.getEnd(), 147);
       Assert.assertEquals(actualMapping, expectedMapping);
@@ -303,7 +304,7 @@ public class SiftsClientTest
   private void populateAtomPositionsNullTest1()
           throws IllegalArgumentException, SiftsException
   {
-      siftsClient.populateAtomPositions(null, null);
+    siftsClient.populateAtomPositions(null, null);
   }
 
   @Test(
@@ -337,7 +338,7 @@ public class SiftsClientTest
     expectedExceptions = SiftsException.class)
   public void getValidSourceDBRefExceptionTest() throws SiftsException
   {
-      SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
+    SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
     try
     {
       siftsClient.getValidSourceDBRef(invalidTestSeq);
@@ -386,8 +387,8 @@ public class SiftsClientTest
               testSeq, testPDBId, "A");
       String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
               + "Method: SIFTS\n\n"
-              + "P00221 :  1 - 97 Maps to \n"
-              + "1A70|A :  51 - 147\n\n"
+              + "P00221 :  51 - 147 Maps to \n"
+              + "1A70|A :  1 - 97\n\n"
               + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
               + "       |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
               + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n"
@@ -448,7 +449,7 @@ public class SiftsClientTest
   }
 
   @Test(groups = { "Functional" })
-  public void getEntityByMostOptimalMatchedIdTest()
+  public void getEntityByMostOptimalMatchedIdTest1()
   {
     SiftsClient siftsClientX = null;
     PDBfile pdbFile;
@@ -471,4 +472,34 @@ public class SiftsClientTest
     Assert.assertEquals(entityD.getEntityId(), "D");
 
   }
+
+  @Test(groups = { "Functional" })
+  public void getEntityByMostOptimalMatchedIdTest2()
+  {
+    // This test is for a SIFTS file in which entity A should map to chain P for
+    // the given PDB Id. All the other chains shouldn't be mapped as there are
+    // no SIFTS entity records for them.
+    SiftsClient siftsClientX = null;
+    PDBfile pdbFile;
+    try
+    {
+      pdbFile = new PDBfile(false, false, false,
+              "test/jalview/io/3ucu.cif", AppletFormatAdapter.FILE);
+      siftsClientX = new SiftsClient(pdbFile);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P");
+    Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A");
+    Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R");
+    Assert.assertEquals(entityA.getEntityId(), "A");
+    Assert.assertNotEquals(entityR, "A");
+    Assert.assertNotEquals(entityP, "A");
+    Assert.assertNotEquals(entityR, "R");
+    Assert.assertNotEquals(entityP, "P");
+    Assert.assertNull(entityR);
+    Assert.assertNull(entityP);
+
+  }
 }